From chemistry-request@server.ccl.net Sun Sep 16 22:19:31 2001 Received: from mercury.sunesis.com ([64.240.200.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8H2JR312282 for ; Sun, 16 Sep 2001 22:19:31 -0400 content-class: urn:content-classes:message Subject: Support Open-Source! (was RE: Chime Encryption) MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Sun, 16 Sep 2001 19:15:39 -0700 Message-ID: X-MimeOLE: Produced By Microsoft Exchange V6.0.4712.0 X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Chime Encryption Thread-Index: AcE+FaoYdnnJR52sRXKJ93g9QP1khwA6OFVw From: "DeLano, Warren" To: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f8H2JV312291 The Chime encryption issue is one more reason why we should support open-source development in computational chemistry. Hear me out... What is going on is that both MDL and CamSoft recognize the utility (and profit potential) for a tool which allows chemists to enter structures onto a web page and then transfer them to a server. The corresponding function of retrieving structures from a database server and displaying them in a web-page is also quite valuable. Quite sensibly, both companies don't want their FREE plug-ins to have this capacity, and their software license agreements may even prohibit such usage. They want you to pay for those valuable capabilities by purchasing the professional plug-ins (or a corresponding encryption-capable server-license). Even though you can most-likely defeat the protections in the FREE plug-ins, actually using them in this manner would be illegal! So how about nurturing a free and open-source alternative? 8-> Since plug-in support has been dropped from the latest version of Internet Explorer, it is now clearly in the interest of both academia and the pharmaceutical industry to FULLY SUPPORT development of a free and open-source chemical ActiveX control capable of database interaction > from a web-page. I believe that an ultra-light-weight 2D chemical display tool could be developed in a couple of months by a competent programmer with sufficient motivation. This would obviate 90% of the need for ChimePro and enable hundreds of new educational and industrial applications. Who will tackle this? You would effectively be creating the "Linux kernel" of chemical informatics! Furthermore, based on my work with PyMOL http://www.pymol.org, I think that an ActiveX/OpenGL based replacement for Chime's 3D rendering capability can also be constructed quite rapidly and do far more than Chime ever could. Of couse, building a 2D drawing tool would be more difficult, but JChemPaint http://jchempaint.sourceforge.net is already halfway there! It just needs a few more features and some usability refinement to get it ready for real-world settings. The bottom line is that we need to motivate open-source developers by coordinating support from industry and academia and by targeting specific key functionalities. The results will be well worth whatever contributions are made because the overall return on investment will be huge in light of how much we currently pay to MDL, Accelrys, etc. Please drop me a short (one line!) email if you (or your organization) might be interested in supporting such efforts OR if you are a developer wishing to receive compensation for open-source programming. I'd like to start a discussion about how to best accomplish this and survey the interest level on both sides. Free/open-source software certainly won't replace most commercial products, but competition from open-source in a few key areas will greatly benefit the science by driving down the cost of commerical products and at the same time increasing the quality of all available software. It is in YOUR INTEREST as a computational scientist to support it! Cheers, - Warren -- mailto:warren@delanoscientific.com Warren L. DeLano, Ph.D. Founder DeLano Scientific "Enabling New Science with Advanced Open-Source Software" > -----Original Message----- > From: Jonathan Brecher [mailto:jsb2@camsoft.com] > Sent: Friday, September 14, 2001 1:38 PM > To: jaouad > Cc: chemistry@ccl.net > Subject: CCL:Chime Encryption > > > >I guess I did not explain very well the situation, > >what I did is creating a web page where we use the > >Chime plugin, so that permit us to call isis draw for > >drawing of the structure we want and send it back to > >the browser, now that we have the struture in our FORM > >we submit it to the server by a Post format and try to > >parse it, Here where the problem come, because when we > >parse it we realize that the structure is encrypted > >twice one by the server and that is normal and we can > >deal with it, but the second encryption is Chime one > >and we dont know how to solve that, i was wondering if > >some one did found a solution to that. > > Um... Did you try asking MDL? Seems to me that if they're > encrypting their > data, then maybe they don't *want* you decoding it... > > We're doing something similar with the ChemDraw Plugin. One > version of the > ChemDraw Plugin produces encrypted data; one version produces > unencrypted > data. > > > Jonathan Brecher > CambridgeSoft Corporation > jsb@camsoft.com From chemistry-request@server.ccl.net Mon Sep 17 06:04:42 2001 Received: from yangtze.hku.hk (IDENT:root@[147.8.148.244]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8HA4e304635 for ; Mon, 17 Sep 2001 06:04:41 -0400 Received: from localhost (andy@localhost) by yangtze.hku.hk (8.9.3/8.9.3) with ESMTP id SAA11753 for ; Mon, 17 Sep 2001 18:19:04 +0800 Date: Mon, 17 Sep 2001 18:19:03 +0800 (HKT) From: Ng Man Fai To: Subject: Crystal structure Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everyone, Does anyone know where the crystal structures of pentacene, BDT and 6T can be found? Thanks a lot. Regards, Andy From chemistry-request@server.ccl.net Mon Sep 17 08:38:29 2001 Received: from cpc.pp.molsci.csiro.au (firewall-user@[138.194.241.18]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8HCcS312788 for ; Mon, 17 Sep 2001 08:38:28 -0400 Received: by cpc.pp.molsci.csiro.au; id WAA19228; Mon, 17 Sep 2001 22:36:52 +1000 (EST) Received: from unknown(138.194.245.49) by cpc.pp.molsci.csiro.au via smap (V5.5) id xma019222; Mon, 17 Sep 01 22:36:41 +1000 Received: from localhost (bra369@localhost) by tigger.pp.molsci.csiro.au (8.9.3+Sun/8.9.3) with SMTP id WAA19650 for ; Mon, 17 Sep 2001 22:38:12 +1000 (EST) Date: Mon, 17 Sep 2001 22:38:12 +1000 (EST) From: Kim Branson To: chemistry@ccl.net Subject: lone pairs in sybyl. In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, does anyone know if it possible to add lone pairs to a protein in sybyl and write the coordinates out to a file (mol2)? the add hydrogen command in bioploymer should do this (in addition to adding hydrogen) but it appears not to. cheers kim ______________________________________________________________________ Mr Kim Branson Phd Student Structural Biology Walter and Eliza Hall Institute Royal Parade, Parkville, Melbourne, Victoria Ph 61 03 9662 7136 Email kbranson@wehi.edu.au ______________________________________________________________________ From chemistry-request@server.ccl.net Mon Sep 17 05:33:31 2001 Received: from orionl0.ccf.auth.gr ([155.207.199.31]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8H9XU303610 for ; Mon, 17 Sep 2001 05:33:31 -0400 Received: from chem011 (chem011.chem.auth.gr [155.207.64.94]) by orionl0.ccf.auth.gr (8.11.6/8.11.4/8.11.4) with SMTP id f8H9XTX01154 for ; Mon, 17 Sep 2001 12:33:30 +0300 (EET DST) Organization: Message-ID: <004001c13f5b$78ec2400$5e40cf9b@chem.auth.gr> From: "temper" To: Subject: Broken symmetry calculations Date: Mon, 17 Sep 2001 12:30:58 +0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_003B_01C13F74.9AB42CE0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 This is a multi-part message in MIME format. ------=_NextPart_000_003B_01C13F74.9AB42CE0 Content-Type: text/plain; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable Dear CCLs In the course of the theoretical ab initio treatment of magnetic = exchange in dinuclear transition metal systems some authors use the method of = broken=20 symmetry. Is there anybody to help me in how to do broken symmetry = calculations? Is there any recipe for it? Thank you in advance. Postgraduate (Ph.D) Student Vasilios I. Teberekidis Laboratory of Applied Quantum Chemistry=20 Aristotle University of Thessaloniki (Greece) Tel.:(+30 31) 99 78 20 +30937 66 18 18 E-mail: temper@chem.auth.gr www: http://users.auth.gr/temper ------=_NextPart_000_003B_01C13F74.9AB42CE0 Content-Type: text/html; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable
Dear CCLs
 
In the course of the theoretical ab initio treatment = of=20 magnetic exchange
in dinuclear transition metal systems some authors = use the=20 method of broken
symmetry. Is there anybody to help me in how to do = broken=20 symmetry calculations?
Is there any recipe for it?
 
Thank you in = advance.
 
Postgraduate (Ph.D) Student
Vasilios I.=20 Teberekidis
Laboratory of Applied Quantum Chemistry
Aristotle = University=20 of Thessaloniki (Greece)
Tel.:(+30 31) 99 78=20 20
        +30937 66 18 = 18
E-mail: temper@chem.auth.gr
www: http://users.auth.gr/temper
------=_NextPart_000_003B_01C13F74.9AB42CE0-- From chemistry-request@server.ccl.net Mon Sep 17 02:17:03 2001 Received: from wn1.sci.kun.nl ([131.174.8.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8H6H3319531 for ; Mon, 17 Sep 2001 02:17:03 -0400 Received: from garak.sci.kun.nl by wn1.sci.kun.nl via garak.sci.kun.nl [131.174.9.35] with ESMTP id f8H6Gth03016 (8.11.3/3.19); Mon, 17 Sep 2001 08:16:55 +0200 (MET DST) Received: from egonw by garak.sci.kun.nl with local (Exim 3.32 #1 (Debian)) id 15irml-0000BJ-00; Mon, 17 Sep 2001 08:21:39 +0200 Content-Type: text/plain; charset="iso-8859-1" From: Egon Willighagen Reply-To: egonw@sci.kun.nl To: "DeLano, Warren" Subject: Re: CCL:Support Open-Source! (was Chime Encryption) Date: Mon, 17 Sep 2001 08:21:39 +0200 X-Mailer: KMail [version 1.3.1] References: In-Reply-To: Cc: jchempaint-devel@sourceforge.net, MIME-Version: 1.0 Message-Id: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f8H6H3319532 On Monday 17 September 2001 04:15, you wrote: > Of couse, building a 2D drawing tool would be more difficult, but > JChemPaint http://jchempaint.sourceforge.net is already halfway there! > It just needs a few more features and some usability refinement to get > it ready for real-world settings. Thanx for advertising JChemPaint on CCL! :) Can you list the features and refinements you miss? I think most of the JCP developers are interested in making JCP more usable. At least i am... If you could state the missing stuff, we could see what we can add in the next few weeks/months... BTW, last year i gave a presentation in Washington,DC at ChemInt2000 about a servlet for webservers for more intelligent publishing of chemical data. A prototype is available, and later this year i am going to rewrite the prototype to use CDK (http://cdk.sf.net/), on which JCP-2 is also based. The prototype which i demonstrated on ChemInt 2000 can be downloaded from CVS at http://sdwb.sf.net/ (GPL license). To give a small outline of what the CDK based version will be able to do: - publish structure databases: - JDBC based databases (e.g. MySQL) - directory structure based databases (MDL mol, CML, PDB, etc... formats) - publication of XHTML documents containing CML fragments - dynamically publish it in several formats depending on browser/platform - to develop ActiveX plugin for MS/IE - Chime-plugin for older MS/IE - Java-plugin for Netscape - GIF/PNG picture - etc - user overwrite of this format - support caching Note that some of this stuff is already done by the first prototype. Comments are welcomed. Egon Willighagen From chemistry-request@server.ccl.net Mon Sep 17 10:39:28 2001 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8HEdS315612 for ; Mon, 17 Sep 2001 10:39:28 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.11.2/8.11.2/Guy-12-01-2001) with ESMTP id f8HEdRe14530 for ; Mon, 17 Sep 2001 16:39:27 +0200 (METDST) Received: from lctn.uhp-nancy.fr (host23.lctn.uhp-nancy.fr [193.50.239.30]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id QAA18424 for ; Mon, 17 Sep 2001 16:38:45 +0200 Sender: assfeld@host20.lctn.uhp-nancy.fr Message-ID: <3BA606E0.912D425@lctn.uhp-nancy.fr> Date: Mon, 17 Sep 2001 16:21:20 +0200 From: Xavier ASSFELD Organization: Chimie Theorique X-Mailer: Mozilla 4.51i [en] (X11; I; AIX 4.3) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: P. G. de Gennes citation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, A friend told me that few years ago, the nobel prize laureate, Pierre Gilles De Gennes said something like: "Solid state physic and quantum chemistry are dying sciences." First, I would like to know if it is true that he said something similar. Second, I would greatly appreciate if someone can provide me the exact citation and the exact reference. Thank you very much in advance. -- ...Xav WARNING! NEW E-MAIL ADDRESS ! (u-nancy changed to uhp-nancy) Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Mon Sep 17 16:28:02 2001 Received: from mail1.ats.rochester.edu (IDENT:998@[128.151.224.31]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8HKS2321792 for ; Mon, 17 Sep 2001 16:28:02 -0400 Received: from localhost (weiz@localhost) by mail1.ats.rochester.edu (8.11.6/8.11.6) with ESMTP id f8HKSL41413599 for ; Mon, 17 Sep 2001 16:28:21 -0400 (EDT) Date: Mon, 17 Sep 2001 16:28:21 -0400 From: Wei Zhuang X-Sender: weiz@mail1.ats.rochester.edu To: chemistry@ccl.net Subject: torsional parameters in MM2/MM3 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi,all: the formula of calculating torsional energy in MM3 is like: E=(k'/2)(1+cosA)+(k"/2)(1-cos2A)+(k'''/2)(1+cos3A). so I need 3 parameters:k',k",k''',but in the oringinal papers, when they talked about the types including O and S, they only gave one parameter,could anybody tell me why?thanks. regards wei zhuang e-mail:weiz@mail.rochester.edu office phone:716-2750387 From chemistry-request@server.ccl.net Mon Sep 17 09:54:26 2001 Received: from eyou.com ([61.136.62.73]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f8HDrs314536 for ; Mon, 17 Sep 2001 09:54:25 -0400 Received: (qmail 13803 invoked from network); 17 Sep 2001 21:53:52 +0800 Received: from unknown (HELO eyou.com) (172.16.2.1) by 172.16.1.1 with SMTP; 17 Sep 2001 21:53:52 +0800 Received: (qmail 99708 invoked by uid 65534); 17 Sep 2001 21:53:54 +0800 Date: 17 Sep 2001 21:53:54 +0800 Message-ID: <20010917215354.99707.qmail@eyou.com> From: "王建国" To: chemistry@ccl.net Reply-To: "王建国" Subject: ask for help hello, Everyone. I am a new user of DOCK4.0 and AutoDock3.0. I met with some trouble after installation of both programmes. For DOCK4.0, it needs f77 and gcc to makefile to compile it, I downloaded gcc > from the SGI web, but I couldn't find a website that provided f77 compiler freeware. If someone knows where I can download the freeware of f77 compiler, would you do me a favor by telling me the website? For QCPE-MS, where can I get a suitable program that is free of charge? For AutoDock3.0, I tried to run the program as instruction,I got the warning as follow: indy2 15% mol2topdbqs epsps.mol2 gawk - Command not found Cannot open /mol2fftopdbq.awk: No such file or directory Source line number 1 Context is >>> <<< addsol - Command not found indy2 16% deftors ligand.mol2 Starting Autotors... using command "autotors -A +15.0 -a -h -m ligand.mol2 ligand.pdbq" autotors - Command not found Checking charges... Sorting "ligand" by residue number. Cannot open ligand: No such file or directory Checking charges in "ligand", using "chckqs"; All errors held in "ligand.err" Finished. Created ligand.pdbq and ligand.err If ligand.err is not empty, check the partial charges assigned to ligand.pdbq I know there must be something wrong with my program, but I am not familiar with the compiling programs. I want to know how to install and run the program with ease. My workstation is in SGI environment with IRIX6.5 and UNIX system. Thank you. Sincerely Yours, Jianguo Wang, Elemento-Organic Chemistry Institute, National Pesticide Engineering Research Center, Tianjin, 300071. P. R. China. e-mail: nkwjg@eyou.com voice: 86-22-23503705 fax: 86-22-23505948 --http://www.eyou.com --稳定可靠的免费电子信箱 语音邮件 移动书签 日历服务 网络存储...亿邮未尽 From chemistry-request@server.ccl.net Mon Sep 17 18:51:17 2001 Received: from physics.lsu.edu ([130.39.182.96]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8HMpH324856 for ; Mon, 17 Sep 2001 18:51:17 -0400 Received: from localhost (vani@localhost) by physics.lsu.edu (8.9.2/8.9.2) with ESMTP id RAA21749 for ; Mon, 17 Sep 2001 17:49:14 -0500 (CDT) Date: Mon, 17 Sep 2001 17:49:14 -0500 (CDT) From: Vemparala Satyavani To: chemistry@ccl.net Subject: non bonded interactions in proteins. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, i have a question regarding the criterion for selecting the atoms in protein which will be involved in non bonded interactions. While simulating polymers, the criterion is usually, atoms belonging to seperate chains, or on the same chain, seperated by some atoms(usually>3). is there a similar criterion in proteins? thanks vani